From 1982 to 1984, he was a fellow in neurology and immunology at
Harvard Medical School in
Boston, Massachusetts. He was one of the first post-doctoral fellows of
Howard L. Weiner, and began to work in his lab on multiple sclerosis. In 1984, he joined the faculty of Harvard Medical School in the department of Neurology. He stayed on in Weiner's laboratory, becoming a
principal investigator. The company went public in 1993 with Henri Termeer and others on the Board of Directors. In 2000, he was appointed to an
endowed professorship and became the Breakstone Professor of Neurology at Harvard. In 2015, Hafler was appointed to the newly created Edgerly Professorship in Neurology at Yale. This endowed professorship was provided by William S. and Lois Stiles Edgerly who had long supported research in multiple sclerosis. In 2018 he was elected to membership in the National Academy of Medicine with the citation "For seminal discoveries defining the pathogenesis of multiple sclerosis (MS), including identification of autoreactive T cells and mechanisms that underlie their dysregulation, and the discovery of susceptibility genes that lead to MS." ==Awards and honors==